VIGGS:Variant information

Chr03:4606852 - 4610464

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SNPs

Position	Ref.	Alt.	Depth	Score	Freq. Of Alt.	Effect	Species
4607016	T	A	52	2294.77	1.00	DOWNSTREAM(\|1452\|\|None\|Vigan.03G048200.01), SYNONYMOUS_CODING(SILENT\|tcT/tcA\|S24\|None\|Vigan.03G048400.01), UPSTREAM(\|1452\|\|None\|Vigan.03G048300.01)	Vigna nepalensis
4607022	T	C	49	2218.77	1.00	DOWNSTREAM(\|1458\|\|None\|Vigan.03G048200.01), SYNONYMOUS_CODING(SILENT\|ttT/ttC\|F26\|None\|Vigan.03G048400.01), UPSTREAM(\|1458\|\|None\|Vigan.03G048300.01)	Vigna nepalensis
4607205	A	T	46	1812.77	1.00	DOWNSTREAM(\|1641\|\|None\|Vigan.03G048200.01), INTRON(\|\|\|None\|Vigan.03G048400.01), UPSTREAM(\|1641\|\|None\|Vigan.03G048300.01)	Vigna nepalensis
4607257	A	C	46	1858.77	1.00	DOWNSTREAM(\|1693\|\|None\|Vigan.03G048200.01), INTRON(\|\|\|None\|Vigan.03G048400.01), UPSTREAM(\|1693\|\|None\|Vigan.03G048300.01)	Vigna nepalensis
4607363	A	G	45	1720.77	1.00	DOWNSTREAM(\|1799\|\|None\|Vigan.03G048200.01), NON_SYNONYMOUS_CODING(MISSENSE\|gAt/gGt\|D77G\|None\|Vigan.03G048400.01), UPSTREAM(\|1799\|\|None\|Vigan.03G048300.01)	Vigna nepalensis
4607472	A	G	57	2261.77	1.00	DOWNSTREAM(\|1908\|\|None\|Vigan.03G048200.01), INTRON(\|\|\|None\|Vigan.03G048400.01), UPSTREAM(\|1908\|\|None\|Vigan.03G048300.01)	Vigna nepalensis
4607607	G	C	59	2408.77	1.00	DOWNSTREAM(\|2043\|\|None\|Vigan.03G048200.01), NON_SYNONYMOUS_CODING(MISSENSE\|Gtt/Ctt\|V120L\|None\|Vigan.03G048400.01), UPSTREAM(\|2043\|\|None\|Vigan.03G048300.01)	Vigna nepalensis
4607668	A	G	51	2105.77	1.00	DOWNSTREAM(\|2104\|\|None\|Vigan.03G048200.01), INTRON(\|\|\|None\|Vigan.03G048400.01), SPLICE_SITE_REGION(\|\|\|None\|Vigan.03G048400.01), UPSTREAM(\|2104\|\|None\|Vigan.03G048300.01)	Vigna nepalensis
4607740	G	A	51	2328.77	1.00	DOWNSTREAM(\|2176\|\|None\|Vigan.03G048200.01), INTRON(\|\|\|None\|Vigan.03G048400.01), UPSTREAM(\|2176\|\|None\|Vigan.03G048300.01)	Vigna nepalensis
4607749	T	A	49	2262.77	1.00	DOWNSTREAM(\|2185\|\|None\|Vigan.03G048200.01), INTRON(\|\|\|None\|Vigan.03G048400.01), UPSTREAM(\|2185\|\|None\|Vigan.03G048300.01)	Vigna nepalensis
4607750	A	G	48	2220.77	1.00	DOWNSTREAM(\|2186\|\|None\|Vigan.03G048200.01), INTRON(\|\|\|None\|Vigan.03G048400.01), UPSTREAM(\|2186\|\|None\|Vigan.03G048300.01)	Vigna nepalensis
4607768	A	T	49	2121.77	1.00	DOWNSTREAM(\|2204\|\|None\|Vigan.03G048200.01), INTRON(\|\|\|None\|Vigan.03G048400.01), UPSTREAM(\|2204\|\|None\|Vigan.03G048300.01)	Vigna nepalensis
4607795	G	T	48	1927.77	1.00	DOWNSTREAM(\|2231\|\|None\|Vigan.03G048200.01), DOWNSTREAM(\|4989\|\|None\|Vigan.03G048500.01), INTRON(\|\|\|None\|Vigan.03G048400.01), UPSTREAM(\|2231\|\|None\|Vigan.03G048300.01)	Vigna nepalensis
4607885	A	G	53	2359.77	1.00	DOWNSTREAM(\|2321\|\|None\|Vigan.03G048200.01), DOWNSTREAM(\|4899\|\|None\|Vigan.03G048500.01), INTRON(\|\|\|None\|Vigan.03G048400.01), UPSTREAM(\|2321\|\|None\|Vigan.03G048300.01), UPSTREAM(\|4994\|\|None\|Vigan.03G048600.01)	Vigna nepalensis
4607902	T	G	55	2446.77	1.00	DOWNSTREAM(\|2338\|\|None\|Vigan.03G048200.01), DOWNSTREAM(\|4882\|\|None\|Vigan.03G048500.01), INTRON(\|\|\|None\|Vigan.03G048400.01), UPSTREAM(\|2338\|\|None\|Vigan.03G048300.01), UPSTREAM(\|4977\|\|None\|Vigan.03G048600.01)	Vigna nepalensis
4607914	A	G	53	2512.77	1.00	DOWNSTREAM(\|2350\|\|None\|Vigan.03G048200.01), DOWNSTREAM(\|4870\|\|None\|Vigan.03G048500.01), INTRON(\|\|\|None\|Vigan.03G048400.01), UPSTREAM(\|2350\|\|None\|Vigan.03G048300.01), UPSTREAM(\|4965\|\|None\|Vigan.03G048600.01)	Vigna nepalensis
4607963	G	T	52	2140.77	1.00	DOWNSTREAM(\|2399\|\|None\|Vigan.03G048200.01), DOWNSTREAM(\|4821\|\|None\|Vigan.03G048500.01), INTRON(\|\|\|None\|Vigan.03G048400.01), UPSTREAM(\|2399\|\|None\|Vigan.03G048300.01), UPSTREAM(\|4916\|\|None\|Vigan.03G048600.01)	Vigna nepalensis
4608174	G	T	54	2200.77	1.00	DOWNSTREAM(\|2610\|\|None\|Vigan.03G048200.01), DOWNSTREAM(\|4610\|\|None\|Vigan.03G048500.01), INTRON(\|\|\|None\|Vigan.03G048400.01), UPSTREAM(\|2610\|\|None\|Vigan.03G048300.01), UPSTREAM(\|4705\|\|None\|Vigan.03G048600.01)	Vigna nepalensis
4608215	C	G	48	2119.77	1.00	DOWNSTREAM(\|2651\|\|None\|Vigan.03G048200.01), DOWNSTREAM(\|4569\|\|None\|Vigan.03G048500.01), INTRON(\|\|\|None\|Vigan.03G048400.01), UPSTREAM(\|2651\|\|None\|Vigan.03G048300.01), UPSTREAM(\|4664\|\|None\|Vigan.03G048600.01)	Vigna nepalensis
4608216	C	T	47	2119.77	1.00	DOWNSTREAM(\|2652\|\|None\|Vigan.03G048200.01), DOWNSTREAM(\|4568\|\|None\|Vigan.03G048500.01), INTRON(\|\|\|None\|Vigan.03G048400.01), UPSTREAM(\|2652\|\|None\|Vigan.03G048300.01), UPSTREAM(\|4663\|\|None\|Vigan.03G048600.01)	Vigna nepalensis
4608253	C	T	48	1918.77	1.00	DOWNSTREAM(\|2689\|\|None\|Vigan.03G048200.01), DOWNSTREAM(\|4531\|\|None\|Vigan.03G048500.01), INTRON(\|\|\|None\|Vigan.03G048400.01), UPSTREAM(\|2689\|\|None\|Vigan.03G048300.01), UPSTREAM(\|4626\|\|None\|Vigan.03G048600.01)	Vigna nepalensis
4608265	A	T	46	1828.77	1.00	DOWNSTREAM(\|2701\|\|None\|Vigan.03G048200.01), DOWNSTREAM(\|4519\|\|None\|Vigan.03G048500.01), INTRON(\|\|\|None\|Vigan.03G048400.01), UPSTREAM(\|2701\|\|None\|Vigan.03G048300.01), UPSTREAM(\|4614\|\|None\|Vigan.03G048600.01)	Vigna nepalensis
4608316	T	A	51	1961.77	1.00	DOWNSTREAM(\|2752\|\|None\|Vigan.03G048200.01), DOWNSTREAM(\|4468\|\|None\|Vigan.03G048500.01), NON_SYNONYMOUS_CODING(MISSENSE\|caT/caA\|H183Q\|None\|Vigan.03G048400.01), UPSTREAM(\|2752\|\|None\|Vigan.03G048300.01), UPSTREAM(\|4563\|\|None\|Vigan.03G048600.01)	Vigna nepalensis
4608631	C	A	51	2033.77	1.00	DOWNSTREAM(\|3067\|\|None\|Vigan.03G048200.01), DOWNSTREAM(\|4153\|\|None\|Vigan.03G048500.01), INTRON(\|\|\|None\|Vigan.03G048400.01), UPSTREAM(\|3067\|\|None\|Vigan.03G048300.01), UPSTREAM(\|4248\|\|None\|Vigan.03G048600.01)	Vigna nepalensis
4609205	T	C	68	2986.77	1.00	DOWNSTREAM(\|3579\|\|None\|Vigan.03G048500.01), DOWNSTREAM(\|3641\|\|None\|Vigan.03G048200.01), INTRON(\|\|\|None\|Vigan.03G048400.01), UPSTREAM(\|3641\|\|None\|Vigan.03G048300.01), UPSTREAM(\|3674\|\|None\|Vigan.03G048600.01)	Vigna nepalensis
4609211	T	C	70	3114.77	1.00	DOWNSTREAM(\|3573\|\|None\|Vigan.03G048500.01), DOWNSTREAM(\|3647\|\|None\|Vigan.03G048200.01), INTRON(\|\|\|None\|Vigan.03G048400.01), UPSTREAM(\|3647\|\|None\|Vigan.03G048300.01), UPSTREAM(\|3668\|\|None\|Vigan.03G048600.01)	Vigna nepalensis
4609519	T	C	69	647.77	0.29	DOWNSTREAM(\|3265\|\|None\|Vigan.03G048500.01), DOWNSTREAM(\|3955\|\|None\|Vigan.03G048200.01), INTRON(\|\|\|None\|Vigan.03G048400.01), UPSTREAM(\|3360\|\|None\|Vigan.03G048600.01), UPSTREAM(\|3955\|\|None\|Vigan.03G048300.01)	Vigna nepalensis
4609527	G	A	78	714.77	0.27	DOWNSTREAM(\|3257\|\|None\|Vigan.03G048500.01), DOWNSTREAM(\|3963\|\|None\|Vigan.03G048200.01), INTRON(\|\|\|None\|Vigan.03G048400.01), UPSTREAM(\|3352\|\|None\|Vigan.03G048600.01), UPSTREAM(\|3963\|\|None\|Vigan.03G048300.01)	Vigna nepalensis
4609532	G	A	91	1131.77	0.34	DOWNSTREAM(\|3252\|\|None\|Vigan.03G048500.01), DOWNSTREAM(\|3968\|\|None\|Vigan.03G048200.01), INTRON(\|\|\|None\|Vigan.03G048400.01), UPSTREAM(\|3347\|\|None\|Vigan.03G048600.01), UPSTREAM(\|3968\|\|None\|Vigan.03G048300.01)	Vigna nepalensis
4609536	G	C	93	1158.77	0.34	DOWNSTREAM(\|3248\|\|None\|Vigan.03G048500.01), DOWNSTREAM(\|3972\|\|None\|Vigan.03G048200.01), INTRON(\|\|\|None\|Vigan.03G048400.01), UPSTREAM(\|3343\|\|None\|Vigan.03G048600.01), UPSTREAM(\|3972\|\|None\|Vigan.03G048300.01)	Vigna nepalensis
4609555	A	C	97	2373.77	0.62	DOWNSTREAM(\|3229\|\|None\|Vigan.03G048500.01), DOWNSTREAM(\|3991\|\|None\|Vigan.03G048200.01), INTRON(\|\|\|None\|Vigan.03G048400.01), UPSTREAM(\|3324\|\|None\|Vigan.03G048600.01), UPSTREAM(\|3991\|\|None\|Vigan.03G048300.01)	Vigna nepalensis
4609812	A	G	88	993.77	0.28	DOWNSTREAM(\|2972\|\|None\|Vigan.03G048500.01), DOWNSTREAM(\|4248\|\|None\|Vigan.03G048200.01), INTRON(\|\|\|None\|Vigan.03G048400.01), UPSTREAM(\|3067\|\|None\|Vigan.03G048600.01), UPSTREAM(\|4248\|\|None\|Vigan.03G048300.01)	Vigna nepalensis
4609965	A	G	41	1841.77	1.00	DOWNSTREAM(\|2819\|\|None\|Vigan.03G048500.01), DOWNSTREAM(\|4401\|\|None\|Vigan.03G048200.01), INTRON(\|\|\|None\|Vigan.03G048400.01), UPSTREAM(\|2914\|\|None\|Vigan.03G048600.01), UPSTREAM(\|4401\|\|None\|Vigan.03G048300.01)	Vigna nepalensis
4609982	G	C	42	1876.77	1.00	DOWNSTREAM(\|2802\|\|None\|Vigan.03G048500.01), DOWNSTREAM(\|4418\|\|None\|Vigan.03G048200.01), INTRON(\|\|\|None\|Vigan.03G048400.01), UPSTREAM(\|2897\|\|None\|Vigan.03G048600.01), UPSTREAM(\|4418\|\|None\|Vigan.03G048300.01)	Vigna nepalensis
4610121	G	T	47	1930.77	1.00	DOWNSTREAM(\|2663\|\|None\|Vigan.03G048500.01), DOWNSTREAM(\|4557\|\|None\|Vigan.03G048200.01), INTRON(\|\|\|None\|Vigan.03G048400.01), UPSTREAM(\|2758\|\|None\|Vigan.03G048600.01), UPSTREAM(\|4557\|\|None\|Vigan.03G048300.01)	Vigna nepalensis
4610455	A	G	65	2569.77	1.00	DOWNSTREAM(\|2329\|\|None\|Vigan.03G048500.01), DOWNSTREAM(\|4891\|\|None\|Vigan.03G048200.01), UPSTREAM(\|2424\|\|None\|Vigan.03G048600.01), UPSTREAM(\|4891\|\|None\|Vigan.03G048300.01), UTR_3_PRIME(\|225\|\|None\|Vigan.03G048400.01)	Vigna nepalensis

Indels

Position	Ref.	Alt.	Depth	Score	Freq. Of Alt.	Effect	Species
4607848	T	TATG	48	2167.73	1.00	DOWNSTREAM(\|2285\|\|None\|Vigan.03G048200.01), DOWNSTREAM(\|4935\|\|None\|Vigan.03G048500.01), INTRON(\|\|\|None\|Vigan.03G048400.01), UPSTREAM(\|2285\|\|None\|Vigan.03G048300.01)	Vigna nepalensis
4608611	C	CCTT	60	2662.73	1.00	DOWNSTREAM(\|3048\|\|None\|Vigan.03G048200.01), DOWNSTREAM(\|4172\|\|None\|Vigan.03G048500.01), INTRON(\|\|\|None\|Vigan.03G048400.01), UPSTREAM(\|3048\|\|None\|Vigan.03G048300.01), UPSTREAM(\|4267\|\|None\|Vigan.03G048600.01)	Vigna nepalensis
4608919	CT	C	56	1644.73	1.00	DOWNSTREAM(\|3356\|\|None\|Vigan.03G048200.01), DOWNSTREAM(\|3864\|\|None\|Vigan.03G048500.01), INTRON(\|\|\|None\|Vigan.03G048400.01), UPSTREAM(\|3356\|\|None\|Vigan.03G048300.01), UPSTREAM(\|3959\|\|None\|Vigan.03G048600.01)	Vigna nepalensis
4609085	T	TTA	62	2724.73	1.00	DOWNSTREAM(\|3522\|\|None\|Vigan.03G048200.01), DOWNSTREAM(\|3698\|\|None\|Vigan.03G048500.01), INTRON(\|\|\|None\|Vigan.03G048400.01), UPSTREAM(\|3522\|\|None\|Vigan.03G048300.01), UPSTREAM(\|3793\|\|None\|Vigan.03G048600.01)	Vigna nepalensis
4609264	A	AT	49	1324.73	0.98	DOWNSTREAM(\|3519\|\|None\|Vigan.03G048500.01), DOWNSTREAM(\|3701\|\|None\|Vigan.03G048200.01), INTRON(\|\|\|None\|Vigan.03G048400.01), UPSTREAM(\|3614\|\|None\|Vigan.03G048600.01), UPSTREAM(\|3701\|\|None\|Vigan.03G048300.01)	Vigna nepalensis
4609486	TAG	T	58	224.73	0.17	DOWNSTREAM(\|3297\|\|None\|Vigan.03G048500.01), DOWNSTREAM(\|3923\|\|None\|Vigan.03G048200.01), INTRON(\|\|\|None\|Vigan.03G048400.01), UPSTREAM(\|3392\|\|None\|Vigan.03G048600.01), UPSTREAM(\|3923\|\|None\|Vigan.03G048300.01)	Vigna nepalensis
4609529	T	TTTAAATCCTAAACCC	81	1080.73	0.27	DOWNSTREAM(\|3254\|\|None\|Vigan.03G048500.01), DOWNSTREAM(\|3966\|\|None\|Vigan.03G048200.01), INTRON(\|\|\|None\|Vigan.03G048400.01), UPSTREAM(\|3349\|\|None\|Vigan.03G048600.01), UPSTREAM(\|3966\|\|None\|Vigan.03G048300.01)	Vigna nepalensis
4609546	G	GTAAA	97	1269.73	0.33	DOWNSTREAM(\|3237\|\|None\|Vigan.03G048500.01), DOWNSTREAM(\|3983\|\|None\|Vigan.03G048200.01), INTRON(\|\|\|None\|Vigan.03G048400.01), UPSTREAM(\|3332\|\|None\|Vigan.03G048600.01), UPSTREAM(\|3983\|\|None\|Vigan.03G048300.01)	Vigna nepalensis
4609548	TGCAA	T	96	1234.73	0.33	DOWNSTREAM(\|3235\|\|None\|Vigan.03G048500.01), DOWNSTREAM(\|3985\|\|None\|Vigan.03G048200.01), INTRON(\|\|\|None\|Vigan.03G048400.01), UPSTREAM(\|3330\|\|None\|Vigan.03G048600.01), UPSTREAM(\|3985\|\|None\|Vigan.03G048300.01)	Vigna nepalensis
4609818	G	GAGTATGTTTTCTTGTTTGATC	84	780.73	0.29	DOWNSTREAM(\|2965\|\|None\|Vigan.03G048500.01), DOWNSTREAM(\|4255\|\|None\|Vigan.03G048200.01), INTRON(\|\|\|None\|Vigan.03G048400.01), UPSTREAM(\|3060\|\|None\|Vigan.03G048600.01), UPSTREAM(\|4255\|\|None\|Vigan.03G048300.01)	Vigna nepalensis